I have tested the t4-toluene example and it worked well. But when I use my own system
, it hasn't work quite well. In this system, the ligand is greatly larger than toluene and is in the solvent but not in protein pocket. And I has not freeze any groups. The protocolWork turned nan after performing TranslationMove in NCMC show as following:
#"Iter" "Progress (%)" "Step" "alchemicalLambda" "protocolWork" "Speed (ns/day)" "Time Remaining"
ncmc: 0 5.0% 25 0.05 39.08851538888597 0 --
ncmc: 0 10.0% 50 0.1 70.96068947520838 26.7 0:05
ncmc: 0 15.0% 75 0.15 94.11311782093316 28.2 0:05
ncmc: 0 20.0% 100 0.2 108.8464813136671 26.5 0:05
ncmc: 0 25.0% 125 0.25 108.8464813136671 26.5 0:04
ncmc: 0 30.0% 150 0.3 108.9467082762027 26.4 0:04
ncmc: 0 35.0% 175 0.35 108.9467082762027 26.2 0:04
ncmc: 0 40.0% 200 0.4 108.9467082762027 25.8 0:04
ncmc: 0 45.0% 225 0.45 108.8464813136671 25.9 0:03
ncmc: 0 50.0% 250 0.5 109.04693523873831 22.5 0:03
Performing RandomLigandRotationMove...
ncmc: 0 55.0% 275 0.55 nan 16.8 0:04
ncmc: 0 60.0% 300 0.6 nan 13.6 0:05
ncmc: 0 65.0% 325 0.65 nan 11.8 0:05
ncmc: 0 70.0% 350 0.7 nan 10.8 0:04
ncmc: 0 75.0% 375 0.75 nan 10.1 0:04
ncmc: 0 80.0% 400 0.8 nan 9.52 0:03
ncmc: 0 85.0% 425 0.85 nan 9.08 0:02
ncmc: 0 90.0% 450 0.9 nan 8.73 0:01
ncmc: 0 95.0% 475 0.95 nan 8.45 0:01
ERROR: [simulation._stepNCMC] Particle coordinate is nan
So I wander how this phenomenon comes into being. Maybe it is the clash between ligand and solvent that cause this problem?
I have tested the t4-toluene example and it worked well. But when I use my own system
, it hasn't work quite well. In this system, the ligand is greatly larger than toluene and is in the solvent but not in protein pocket. And I has not freeze any groups. The protocolWork turned nan after performing TranslationMove in NCMC show as following:
So I wander how this phenomenon comes into being. Maybe it is the clash between ligand and solvent that cause this problem?